Data substructural searching

Factual databases may provide the electronic version of printed catalogs on chemical compoimds. The catalogs of different suppliers of chemicals serve to identify chemical compounds with their appropriate synonyms, molecular formulas, molecular weight, structure diagrams, and - of course - the price. Sometimes the data are linked to other databases that contain additional information. Structure and substructure search possibihties have now been included in most of the databases of chemical suppliers. 

The Web-based graphical user interface permits a choice from numerous criteria and the performance of rapid searches. This service, based on the chemistry information toolkit CACTVS, provides complex Boolean searches. Flexible substructure searches have also been implemented. Users can conduct 3D pharmacophore queries in up to 25 conformations pre-calculated for each compound. Numerous output formats as well as 2D and 3D visuaHzation options are supplied. It is possible to export search results in various forms and with choices for data contents in the exported files, for structure sets ranging in size from a single compound to the entire database. Additional information and down-loadable files (in various formats) can be obtained from this service. 

Current chemical information systems offer three principal types of search facility. Structure search involves the search of a file of compounds for the presence or absence of a specified query compound, for example, to retrieve physicochemical data associated with a particular substance. Substructure search involves the search of a file of compounds for all molecules containing some specified query substructure of interest. Finally, similarity search involves the search of a file of compounds for those molecules that are most similar to an input query molecule, using some quantitative definition of structural similarity. 

Second, considerable effort has been expended to create 13C NMR reference data systems that will enable spectroscopists to extract structural information from their experimental results by comparing them with documented spectra of related compounds data banks stored in computers have been compiled and are accessible for substructure searches (510-519). The advent of these facilities means that SCS evaluations have been-at least in principle-outstripped in an important field of their application, namely in their use for establishing molecular constitution and assigning signals. In cases of doubt one should rely... 

If one s purpose is to determine only the presence or absence in a data base of a specific structure, this can be accomplished with the search option IDENT , as is shown in Figure 11. This program hash-encodes the query structure connection table and searches through a file of hash-encoded connection table for an exact match. The search, which is very fast by substructure search standards, has been designed specifically for those users who, to comply with the Toxic Substances Control Act [26l have to determine the presence or absence of specific compounds in Environmental Protection Agency files. 

D similarity and substructure searching are among the most widely used methods for mining structural data (9). The basic principle of these methods is that compounds with structural features in common will have similar properties,... 

Both DIVA and RS3 provide some functionality in terms of substructure searches (SSS), although it is somewhat limited. For example, DIVA searches can only be performed on data that have already been queried from the database ). This pre-queried data need to be readily available to DIVA either via RS3 or as an SD file. In the case of RS3, the inclusion of multiple data sources (e.g., searching the corporate database and an external vendor library) is not trivial. As a result, while DIVA and RS3 are very useful for SSS under certain conditions, they are not as robust when compared to the Pipeline Pilot protocol. 

The information retrieval in MAECIS is accomplished using one of three available commands SHOW, FIND, or SEARCH. The SHOW command is the simplest one to use and requires only a code number or registry number. It allows the user to retrieve all chemical structures and associated information stored under a particular code number. In most cases this fulfills the user s needs. The FIND command is used for complex searches involving various combinations of multiple data fields, handles substructure searching. Queries such structures with a molecular weight between 200 and 250 containing an ester substructure" are handled by the FIND command. Finally, the SEARCH command is used for chemical structure searches. This search takes only seconds and allows the chemist to determine if a particular molecule is already in the database. 

Data storage and querying are the most fundamental requirements of all informatics systems. Thanks to the Oracle Extensibility Framework (a.k.a. Oracle Data Cartridge Technology), chemical structure data can be stored and queried using direct SQL and special query operators, such as substructure search, flexmatch search, similarity search, and formula search. Also, some indexing techniques make these otherwise slow searches fast. Detailed discussions about these databases and cartridges are beyond the scope of this book. Please refer to the vendor s website and product documentation for more information. 

CDD has developed and deployed a robust preliminary public antimalarial database from five sources which hosts data on approximately 16,000 public compounds. The growth of this database has fostered several key antimalarial discovery collaborations between CDD users. A substructure search for the known chemo-sensitizer substructure led to the identification of hundreds of compounds for laboratory evaluation by the laboratories of... 

Binary Data. Data stored in a file or database that is not chemist-readable, and usually cannot be converted to printable characters. Examples include connection table storage in a database, substructure search keys, and a graphics image of a structure. Note that some other data that is also not chemist-readable, like certain linear notations (e.g., a Chime string), may be made up of printable characters and is not strictly binary data. 

Data Cartridge. A popular term for user-customizable search "operators" that can be added to the SQL language of a relational database system. An example in chemical information is the addition of a substructure search (SSS) operator to integrate this type of search directly into a relational database search. One advantage of this approach is that the search "strategy" that the relational search program applies can take the complexity of the custom operator into account (the "cost") when performing the various search operations. 

Index. A secondary data field generated from one or more primary data fields, to enhance the searching and retrieval of the primary data. An index in a chemical database may be a characteristic of the database, such as Oracle indexes, or it may be a chemistiy-specific index such as a tree index for substructure searching. Indexes require extra space, and they typically must be created and maintained by some administrative process in the database. 

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